Contacts of the helix formed by residues 79 - 96 (chain E) in PDB entry 1OCR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 79 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75E ALA* 5.8 0.7 - - - -
76E GLY 5.3 2.5 - - - +
77E PRO 2.9 19.1 + - - +
78E HIS* 1.3 68.7 - - - +
80E GLU* 1.3 79.0 + - + +
81E ILE 3.4 0.7 - - - -
82E TYR* 4.7 2.1 - - - +
83E PRO* 3.1 24.0 - - - +
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Residues in contact with GLU 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E HIS* 3.5 31.5 - - - +
79E LYS* 1.3 100.8 + - + +
81E ILE* 1.3 66.5 + - - +
82E TYR 3.5 0.2 - - - -
83E PRO* 3.6 5.7 - - - +
84E TYR* 3.5 20.6 + - - +
4I LEU* 5.6 2.5 - - + +
7I PRO* 3.7 27.2 - - + +
8I GLN 5.5 0.2 - - - +
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Residues in contact with ILE 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E VAL* 3.7 35.4 - - + -
75E ALA* 3.8 9.0 - - + -
78E HIS* 3.2 34.0 + - + +
80E GLU* 1.3 77.6 - - - +
82E TYR* 1.3 67.3 + - - +
84E TYR* 3.3 4.7 + - - +
85E VAL* 3.0 21.7 + - + +
7I PRO* 3.8 18.8 - - + -
8I GLN 3.5 20.6 - - - +
9I MET* 3.9 18.6 - - + -
12I LEU* 3.7 20.0 - - + -
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Residues in contact with TYR 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E LEU* 3.5 22.5 + - + +
71E VAL* 4.2 11.2 - - + -
72E LYS* 3.6 48.2 - - + +
75E ALA* 4.6 4.1 - - + +
78E HIS 4.6 1.2 + - - -
79E LYS* 4.3 3.1 + - - +
81E ILE* 1.3 79.3 - - - +
83E PRO* 1.3 67.4 - - + +
85E VAL* 2.7 27.6 + - + +
86E ILE* 2.8 41.3 + - + +
101E PRO* 3.6 16.6 - - - +
102E GLU* 2.8 44.3 + - - -
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Residues in contact with PRO 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E LYS 3.1 24.0 - - - +
80E GLU* 3.6 9.9 - - - +
82E TYR* 1.3 100.0 - - + +
84E TYR* 1.3 55.7 + - - +
86E ILE* 3.4 8.2 + - + +
87E GLN* 2.9 28.6 + - - +
4I LEU* 4.6 16.5 - - + +
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Residues in contact with TYR 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E PRO* 4.0 21.5 - - + +
80E GLU 3.5 12.7 + - - +
81E ILE 3.3 10.3 + - - +
82E TYR 3.1 0.4 - - - -
83E PRO* 1.3 81.4 - - - +
85E VAL* 1.3 69.0 + - + +
87E GLN* 3.2 16.9 + - - +
88E GLU* 3.1 49.8 + - + +
4I LEU* 4.0 16.8 - - + +
5I ALA 3.6 15.3 - - - +
6I LYS* 3.5 47.0 - - + +
7I PRO* 3.5 15.7 - - + -
9I MET* 4.3 9.4 - - - -
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Residues in contact with VAL 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E VAL* 4.8 0.2 - - + -
43E PRO 4.8 0.7 - - - +
45E PRO* 4.3 14.6 - - + -
48E ILE* 4.5 10.8 - - + -
68E LEU* 5.9 0.4 - - + -
71E VAL* 3.9 30.3 - - + -
81E ILE* 3.0 15.1 + - + +
82E TYR* 2.7 13.0 + - + +
84E TYR* 1.3 75.2 - - + +
86E ILE* 1.3 69.5 + - + +
87E GLN 3.1 0.2 + - - -
88E GLU* 3.2 2.8 + - - +
89E LEU* 3.0 43.0 + - + +
9I MET* 3.7 28.9 - - + -
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Residues in contact with ILE 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E LEU* 4.2 22.0 - - + -
82E TYR* 2.8 53.5 + - + +
83E PRO* 3.8 9.4 - - + +
85E VAL* 1.3 76.0 - - + +
87E GLN* 1.3 65.8 + - - +
89E LEU* 3.1 6.3 + - + +
90E ARG* 2.9 47.8 + - + +
93E LEU* 4.2 15.3 - - + +
100E THR* 4.3 11.2 - - + -
102E GLU* 5.1 0.7 - - - +
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Residues in contact with GLN 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E PRO 2.9 14.1 + - - +
84E TYR* 3.2 17.2 - - - +
85E VAL 3.1 0.2 - - - -
86E ILE* 1.3 80.3 - - - +
88E GLU* 1.3 82.9 + - - +
89E LEU 3.3 0.3 + - - -
90E ARG* 3.4 18.8 + - - +
91E PRO* 4.2 3.1 - - - +
2I THR 4.6 0.3 - - - +
3I ALA* 3.5 16.6 - - - +
4I LEU* 3.1 58.0 + - + +
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Residues in contact with GLU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E PRO* 3.8 22.8 - - + +
49E ASP* 5.5 1.0 - - - +
84E TYR* 3.1 45.1 + - + +
85E VAL 3.2 1.1 + - - +
87E GLN* 1.3 107.6 + - - +
89E LEU* 1.3 62.7 + - - +
90E ARG 3.4 0.4 + - - -
91E PRO* 3.8 10.3 - - - +
92E THR* 5.6 0.3 + - - -
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Residues in contact with LEU 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E PRO* 3.6 28.0 - - + +
48E ILE* 3.4 25.4 - - + -
49E ASP* 3.7 27.1 - - + +
52E LEU* 4.1 6.5 - - + -
68E LEU* 3.9 18.8 - - + -
85E VAL* 3.0 35.8 + - + +
86E ILE* 3.1 5.8 + - + +
88E GLU* 1.3 81.2 - - - +
90E ARG* 1.3 63.9 + - - +
91E PRO* 3.3 3.6 - - - -
92E THR* 2.9 9.6 + - - +
93E LEU* 2.8 32.0 + - + +
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Residues in contact with ARG 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ILE* 2.9 28.5 + - + +
87E GLN* 3.6 11.7 - - - +
88E GLU 3.4 0.2 - - - -
89E LEU* 1.3 75.6 - - - +
91E PRO* 1.3 71.5 - - + +
93E LEU* 3.1 25.7 + - - +
94E ASN* 2.8 52.3 + - - +
98E ILE 5.0 2.4 + - - -
100E THR* 4.1 10.7 + - - +
103E GLU* 2.8 33.1 + - - -
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Residues in contact with PRO 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E GLN 4.2 4.5 - - - +
88E GLU 3.8 11.0 - - - +
89E LEU 3.4 3.8 - - - -
90E ARG* 1.3 94.6 - - + +
92E THR* 1.3 59.2 + - - +
94E ASN* 3.2 6.8 + - + +
95E GLU* 2.8 31.5 + - - +
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Residues in contact with THR 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ASP* 2.5 27.9 + - - +
52E LEU* 4.5 18.6 - - + -
53E ARG* 2.7 31.1 + - + +
89E LEU* 2.9 10.3 + - - -
91E PRO* 1.3 76.8 - - - +
93E LEU* 1.3 67.7 + - - +
95E GLU* 4.2 6.7 - - - -
96E LEU* 3.0 42.1 + - + +
98E ILE* 4.6 0.6 - - + +
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Residues in contact with LEU 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 3.9 27.4 - - + -
68E LEU* 4.1 10.5 - - + -
86E ILE* 4.2 20.6 - - + +
89E LEU* 2.8 31.3 + - + +
90E ARG* 3.6 23.1 - - - +
92E THR* 1.3 76.2 - - - +
94E ASN* 1.3 57.6 + - - +
97E GLY* 2.9 24.1 + - - -
98E ILE* 2.9 44.5 + - + +
100E THR* 4.1 23.1 - - + -
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Residues in contact with ASN 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D SER* 5.2 3.5 - - - -
90E ARG* 2.8 45.2 + - - +
91E PRO* 3.4 6.1 - - + +
93E LEU* 1.3 76.2 - - - +
95E GLU* 1.3 66.0 + - - +
97E GLY* 3.3 11.4 + - - -
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Residues in contact with GLU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D SER* 5.2 4.0 + - - -
49D SER* 5.3 2.1 + - - -
53E ARG* 2.9 32.8 + - - -
91E PRO* 2.8 21.2 + - - +
92E THR* 3.3 5.8 + - - +
94E ASN* 1.3 74.9 - - - +
96E LEU* 1.3 71.9 + - + +
97E GLY 3.7 0.3 + - - -
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Residues in contact with LEU 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D SER* 5.2 2.0 - - - -
48D TRP* 3.2 32.5 + - + +
49D SER* 4.7 2.2 - - - -
52E LEU 4.4 4.9 - - - +
53E ARG* 4.1 20.6 - - + +
56E ARG* 4.3 32.7 + - + +
92E THR* 3.0 35.1 + - + +
95E GLU* 1.3 100.7 - - + +
97E GLY* 1.3 63.9 + - - +
98E ILE* 3.4 21.9 + - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il